An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes

Journal of Molecular Structure: THEOCHEM

Volumn 760, Issue 1-3, 2006, Pages 91-98

  Riihimäki, Eva Stina ^a   Martínez, José Manuel ^b   Kloo, Lars ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b UNIVERSITY OF SEVILLE   (Spain)

Author keywords

Molecular dynamics; Non periodic boundary conditions; Prion protein; Solvation model

Indexed keywords

EID: 33644817645     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.theochem.2005.11.027     Document Type: Article

References (49)

1. J. Guenot, and P.A. Kollman Protein Sci. 1 1992 1185
2. M.M. Teeter Annu. Rev. Biophys. Biophys. Chem. 20 1991 577
3. D. Mohanty, R. Elber, D. Thirumalai, D. Beglov, and B. Roux J. Mol. Biol. 272 1997 423
4. K.W. Kratky J. Comput. Phys. 37 1980 205
5. M. Berkowitz, C.L. Brooks III, and S.A. Adelman J. Chem. Phys. 72 1980 3889
6. C.L. Brooks III, M. Berkowitz, and S.A. Adelman J. Chem. Phys. 73 1980 4353
7. S.A. Adelman, and C.L. Brooks III J. Phys. Chem. 86 1982 1511
8. M. Berkowitz, and J.A. McCammon Chem. Phys. Lett. 90 1982 215
9. C.L. Brooks III, and M. Karplus J. Chem. Phys. 79 1983 6312
10. A.T. Brünger, C.L. Brooks III, and M. Karplus Proc. Natl Acad. Sci. USA 82 1985 8458
11. C.L. Brooks III, A. Brünger, and M. Karplus Biopolymers 24 1985 843
12. J. Norberg, and L. Nilsson J. Phys. Chem. 99 1995 14876
13. J. Gsponer, P. Ferrara, and A. Caflisch J. Mol. Graph. Mod. 20 2001 169
14. A. Warshel, and G. King Chem. Phys. Lett. 121 1985 124
15. G. King, and A. Warshel J. Chem. Phys. 91 1989 3647
16. D. Beglov, and B. Roux J. Chem. Phys. 100 1994 9050
17. G. Basu, A. Kitao, A. Kuki, and N. Go J. Phys. Chem. B 102 1998 2076
18. G. Basu, A. Kitao, A. Kuki, and N. Go J. Phys. Chem. B 102 1998 2085
19. M. Nina, D. Beglov, and B. Roux J. Phys. Chem. B 101 1997 5239
20. Y. Sugita, and A. Kitao Proteins 30 1998 388
21. Y. Sugita, and A. Kitao Biophys. J. 75 1998 2178
22. S. Marchand, and B. Roux Proteins 33 1998 265
23. A. Kitao, S. Hayward, and N. Go Proteins 33 1998 496
24. D. Beglov, and B. Roux Biopolymers 35 1995 171
25. V. Lounnas, S.K. Lüdemann, and R.C. Wade Biophys. Chem. 78 1999 157
26. S.R. Kimura, R.C. Brower, C. Zhang, and M. Sugimori J. Chem. Phys. 112 2000 7723
27. A.H. Juffer, and H.J.C. Berendsen Mol. Phys. 79 1993 623
28. R. Sankararamakrishnan, K. Konvicka, E.L. Mehler, and H. Weinstein Int. J. Quantum Chem. 77 2000 174
29. J.W. Essex, and W.L. Jorgensen J. Comput. Chem. 16 1995 951
30. J. Marelius, K. Kolmodin, I. Feierberg, and J. Åqvist J. Mol. Graph. Mod. 16 1998 213
31. Y. Li, G. Krilov, and B.J. Berne J. Phys. Chem. B 109 2005 463
32. P.J. Steinbach, and B.R. Brooks Proc. Natl Acad. Sci. USA 90 1993 9135
33. S. Sen, and L. Nilsson Biophys. J. 77 1999 1782
34. N. Okimoto, K. Yamanaka, A. Suenaga, Y. Hirano, N. Futatsugi, T. Narumi, K. Yasuoka, R. Susukita, T. Koishi, H. Furusawa, A. Kawai, M. Hata, T. Hoshino, and T. Ebisuzaki Chem.-Bio. Informatics J. 3 2003 1
35. J.H. Viles, F.E. Cohen, S.B. Prusiner, D.B. Goodin, P.E. Wright, and H.J. Dyson Proc. Natl Acad. Sci. USA 96 1999 2042
36. M.P. Hornshaw, J.R. McDermott, and J.M. Candy Biochem. Biophys. Res. Commun. 207 1995 621
37. A.M. Thackray, R. Knight, S.J. Haswell, R. Bujdoso, and D.R. Brown Biochem. J. 362 2002 253
38. C.S. Burns, E. Aronoff-Spencer, C.M. Dunham, P. Lario, N.I. Avdievich, W.E. Antholine, M.M. Olmstead, A. Vrielink, G.J. Gerfen, J. Peisach, W.G. Scott, and G.L. Millhauser Biochemistry 41 2002 3991
39. G.S. Jackson, I. Murray, L.L.P. Hosszu, N. Gibbs, J.P. Waltho, A.R. Clarke, and J. Collinge Proc. Natl Acad. Sci. USA 98 2001 8531
40. W. Smith, T.R. Forester, DL_POLY (2.14 version), CCLRC, Daresbury Laboratory, 1995.
41. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman J. Am. Chem. Soc. 117 1995 5179
42. H.J.C. Berendsen, J.R. Grigera, and T.P. Straatsma J. Phys. Chem. 91 1987 6269
43. W.G. Hoover Phys. Rev. A 31 1985 1695
44. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen J. Chem. Phys. 103 1995 8577
45. J.M. Martínez, and L. Martínez J. Comput. Chem. 24 2003 819
46. W. Weber, P.H. Hünenberger, and J.A. McCammon J. Phys. Chem. B 104 2000 3668
47. M.A. Kastenholtz, and P.H. Hünenberger J. Phys. Chem. B 108 2004 774
48. M. Schaefer, C. Bartels, and M. Karplus Theor. Chem. Acc. 101 1999 194
49. R. Mills J. Phys. Chem. 77 1973 685